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There certainly isn't anything that can be done using Reader.
What are you using to convert to PDF? That would be where I'd start looking.
I am using Oracle functions that allow me to extract the entire raw file to the operating system (file123-staging.pdf). This file in not readable (it contains the Oracle header / footer information). I open the file and remove all text before the "%PDF-" string and remove all text after the final "%%EOF" string. The new file is saved to the operating system (file123-fixed.pdf).
When a user opens file123-fixed.pdf, it only works some of the time (approximately 50% of the time).
I have received mixed messages from Oracle. Some people say that the original extracted file contains OLE headers / footers; while others say the the PDF file is a "serialized representation" of the PDF file.
Not really sure what a "serialized representation of a file" is?
I'm not sure what that is either but, this seems to be an Oracle issue and not something that can be fixed using an Adobe product.
Another thing to beware of is that PDF files are binary. If you use an
ordinary text editor, rather than a program or editor designed for
binary, there is a very good change you will damage the binary portion
of the file.